The structure of the end-Cretaceous dinosaur fossil record

This dataset contains underlying data, R scripts, and results for the manuscript titled 'The structure of the end-Cretaceous dinosaur fossil record'. Data S1: Contains data for running analyses, as well as results from analyses to be read into R (.rds format), and R scripts for running analyses. Data were derived from the following sources. Note that not all of these data are included within the datasets stored here. Occurrence dataframes were downloaded from The Paleobiology Database (http://paleobiodb.org(opens in new window)). North American roads compiled by the U.S. Department of Transportation (https://data-usdot.opendata.arcgis.com/datasets/usdot::north-american-roads/about(opens in new window)). MGVF obtained from Broxton, P. D., Zeng, X., Scheftic, W. & Troch, P. A. A MODIS-based global 1-km maximum green vegetation fraction dataset. Journal of applied Meteorology and Climatology 53, 1996–2004 (2014). Rainfall obtained from WorldClim (www.worldclim.org(opens in new window)). Outcrop area obtained from https://macrostrat.org(opens in new window) API. Land cover obtained from U.S. Geological Survey. 1-Kilometer Resolution, North American Land Cover Characteristics, 1992-1993. USGS (2002). All paleoclimate model simulations were carried out using a recent version of the UK MetOffice coupled Atmosphere-Ocean General Circulation Model (AOGCM), HadCM3 (specifically HadCM3L-M2.1D), based on palaeogeographies from Scotese, C. R. & Wright, N. PALEOMAP paleodigital elevation models (PaleoDEMS) for the Phanerozoic. URL: https://www(opens in new window). earthbyte. org/paleodem-resource-scotese-and-wright-2018 (2018). These were also used to construct estimates for Sediment Flux. Occurrences Contains the following four files: Distance_roads.csv: A .csv file containing information about the distance from each collection in the dataset from a dataset of North American roads compiled by the U.S. Department of Transportation. Formations.csv: A .csv file containing information about the geologic formations included within the manuscript, most notably their chronostratigraphic information. occs_tetrapoda_12_06_2024.csv: A .csv file of occurrences downloaded from the PBDB on 12/06/2024, used in analyses. scotesebins.csv: A .csv file of the temporal bins used in this study. R_Scripts Contains nine scripts in R for formatting data, running analyses, and visualising results. 0.Format_covariate_data: R script for formatting covariate data for the project. 0.Functions: R script containing custom functions necessary to run other files. Called directly from other files. 0.Macrostrat_outcrop: R script for obtaining and formatting relevant outcrop data from the Macrostrat API. 1.Setup_occupancy: R script for setting up data for analyses. 2.Running_Multispecies_Sparta: R script to format and run occupancy models with 'Sparta'. 3.Multispecies_Sparta_posterior_checks: R script to perform posterior checks on models run using 'Sparta'. 4.Setup_spOccupancy: R script for setting up data into required format for 'spOccupancy'. Handles both single and multi-season formats. 5.Run_ms_spOccupancy: R script for automatically running multi-season occupancy models using 'spOccupancy'. 6.Generating_figures: R script for generating figures for manuscript. Results Contains the results generated for the manuscript for both Sparta and spOccupancy run occupancy models. Sparta results are saved in either .csv or .rds format. spOccupancy results are saved in .rds format.本数据集包含题为《白垩纪末期恐龙化石记录的结构》的学术论文所依托的基础数据、R语言脚本与分析结果。 数据S1：包含分析运行所需数据、可导入R的分析结果文件（.rds格式），以及分析运行所用的R语言脚本。 本数据集的数据源自以下公开资源，请注意并非所有下述资源均包含于本数据集的存储文件中： 1. 化石出现数据框从古生物学数据库（The Paleobiology Database，http://paleobiodb.org，新窗口打开）下载； 2. 北美道路数据集由美国交通部（U.S. Department of Transportation，https://data-usdot.opendata.arcgis.com/datasets/usdot::north-american-roads/about，新窗口打开）汇编； 3. 最大绿色植被分数（MGVF）数据源自：Broxton, P. D.、Zeng, X.、Scheftic, W. 与 Troch, P. A. 发表于《应用气象与气候学杂志》（Journal of applied Meteorology and Climatology）第53卷第1996–2004页（2014年）的《基于MODIS的全球1公里分辨率最大绿色植被分数数据集》一文； 4. 降水数据源自WorldClim（www.worldclim.org，新窗口打开）； 5. 露头面积数据源自https://macrostrat.org（新窗口打开）的应用程序编程接口（API）； 6. 土地覆盖数据源自：美国地质调查局（U.S. Geological Survey，简称USGS）发布的《1992-1993年北美1公里分辨率土地覆盖特征数据集》（2002年）。 所有古气候模型模拟均采用英国气象局最新版本的耦合大气-海洋环流模型（Atmosphere-Ocean General Circulation Model，简称AOGCM）HadCM3（具体版本为HadCM3L-M2.1D），以Scotese, C. R. 与 Wright, N. 2018年发布的《显生宙古数字高程模型（PaleoDEMS）》的古地理数据为基准开展。上述模拟结果同时被用于构建沉积物通量估算值，相关古地理数据的网址为：https://www.earthbyte.org/paleodem-resource-scotese-and-wright-2018（新窗口打开，2018年）。 Occurrences 本模块包含以下四个文件： 1. Distance_roads.csv：该.csv格式文件记录了本数据集内各化石采集点与美国交通部汇编的北美道路数据集之间的距离信息； 2. Formations.csv：该.csv格式文件包含本学术论文涉及的所有地质地层信息，其中核心内容为各地层的年代地层学数据； 3. occs_tetrapoda_12_06_2024.csv：该.csv格式文件为2024年6月12日从PBDB下载的、用于本研究分析的四足类动物化石出现记录数据； 4. scotesebins.csv：该.csv格式文件包含本研究采用的时间间隔划分方案数据。 R_Scripts 本模块包含9个R语言脚本，用于数据格式化、分析运行与结果可视化： 1. 0.Format_covariate_data：用于格式化本项目协变量数据的R语言脚本； 2. 0.Functions：包含运行其他脚本所需的自定义函数，可被其他脚本直接调用； 3. 0.Macrostrat_outcrop：用于从Macrostrat应用程序编程接口（API）获取并格式化相关露头数据的R语言脚本； 4. 1.Setup_occupancy：用于配置本研究分析所需数据的R语言脚本； 5. 2.Running_Multispecies_Sparta：用于格式化并运行基于'Sparta'的多物种占用模型的R语言脚本； 6. 3.Multispecies_Sparta_posterior_checks：用于对基于'Sparta'运行的占用模型开展后验检验的R语言脚本； 7. 4.Setup_spOccupancy：用于将数据格式化为'spOccupancy'所需格式的R语言脚本，支持单季与多季数据格式； 8. 5.Run_ms_spOccupancy：用于自动运行基于'spOccupancy'的多季物种占用模型的R语言脚本； 9. 6.Generating_figures：用于为本学术论文生成可视化图表的R语言脚本。 Results 本模块包含为本学术论文生成的两类物种占用模型分析结果：基于'Sparta'与基于'spOccupancy'的模型结果。其中'Sparta'模型结果以.csv或.rds格式存储，'spOccupancy'模型结果以.rds格式存储。